gs2crmod 0.9.2 → 0.9.4

data/Gemfile

@@ -2,7 +2,7 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
    gem "coderunner", ">= 0.12.16"
-   gem "ruby-netcdf", ">= 0.6.6.1"
+#   gem "ruby-netcdf", ">= 0.6.6.1"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/VERSION

@@ -1 +1 @@
-0.9.2
+0.9.4

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.9.2"
+  s.version = "0.9.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2013-07-31"
+  s.date = "2013-08-07"
   s.description = "GS2 is a gyrokinetic flux tube initial value turbulence code which can be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated running and analysis of large simulations. This module allows GS2 (and its sister code AstroGK) to harness the power of the CodeRunner framework."
   s.email = "edmundhighcock@sourceforge.net"
   s.extensions = ["ext/extconf.rb"]
@@ -78,7 +78,7 @@ Gem::Specification.new do |s|
   s.licenses = ["GSLv3"]
   s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
-  s.rubygems_version = "1.8.11"
+  s.rubygems_version = "1.8.23"
   s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
 
   if s.respond_to? :specification_version then
@@ -86,14 +86,12 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.12.16"])
-      s.add_runtime_dependency(%q<ruby-netcdf>, [">= 0.6.6.1"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
       s.add_development_dependency(%q<jeweler>, [">= 1.8.4"])
     else
       s.add_dependency(%q<coderunner>, [">= 0.12.16"])
-      s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6.1"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<bundler>, ["> 1.0.0"])
@@ -101,7 +99,6 @@ Gem::Specification.new do |s|
     end
   else
     s.add_dependency(%q<coderunner>, [">= 0.12.16"])
-    s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6.1"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<bundler>, ["> 1.0.0"])

data/lib/gs2crmod/gsl_data.rb

@@ -541,8 +541,9 @@ module GSLVectors
 		Dir.chdir(@directory) do
  # , /kpar_spectrum/
 			#ep 'zero?', (@s_hat_input||@shat)==0.0
-			unless (@s_hat_input||@shat||0.75).abs<1.0e-5
+			unless agk? or (@s_hat_input||@shat||0.0).abs<1.0e-5
 				phi = gsl_vector_complex('phi_along_field_line', options)
+        phi = phi.subvector(0,phi.size-1)
 				#i = 0
 				#phi = phi.collect{|re,im| 
 					#i+=1; GSL::Complex.alloc(Math.sin(0.1*i), Math.cos(0.1*i))+ 
@@ -587,10 +588,11 @@ module GSLVectors
 			end
 			case phi.size%2
 			when 0
-				kpar = GSL::Vector.indgen(phi.size, -(phi.size-2)/2)*dk
+				kpar = GSL::Vector.indgen(phi.size-1, -((phi.size-3)/2))*dk
 			when 1
-				kpar = GSL::Vector.indgen(phi.size, -(phi.size-1)/2)*dk
+				kpar = GSL::Vector.indgen(phi.size-1, -((phi.size-2)/2))*dk
 			end
+      #ep 'kpar', kpar, 'phi.size', phi.size
 
 			#ep 'kpar.class', kpar.class
 			return kpar
@@ -999,9 +1001,9 @@ module GSLMatrices
 			end
 			temp = phi_av = (lkx.keys.map do |kx_index|		
 				if options[:t_index]
-					phi =  netcdf_file.var('phi_t').get({'start' => [0,0,kx_index-1,0, options[:t_index] - 1], 'end' => [-1,-1,kx_index-1,-1, options[:t_index] - 1]})
+					phi =  netcdf_file.var('phi_t').get({'start' => [0,0,kx_index-1,0, options[:t_index] - 1], 'end' => [-1,-2,kx_index-1,-1, options[:t_index] - 1]})
 				else
-					phi = netcdf_file.var('phi').get({'start' => [0, 0, kx_index - 1, 0], 'end' => [-1, -1, kx_index-1, -1]})
+					phi = netcdf_file.var('phi').get({'start' => [0, 0, kx_index - 1, 0], 'end' => [-1, -2, kx_index-1, -1]})
 				end
 				#ep phi.shape
 				phi.reshape(*phi.shape.values_at(0,1,3))
@@ -1010,16 +1012,19 @@ module GSLMatrices
 			phi_t = phi_av.to_a #.map{|arr| arr.transpose}.transpose.map{|a| a.transpose}
 			#ep 'phi_t', phi_t.size, phi_t[0].size, phi_t[0][0].size
 			gvky = gsl_vector('ky')
-			gm = GSL::Matrix.alloc(gvky.size, gsl_vector('theta').size)
+			gm = GSL::Matrix.alloc(gvky.size, gsl_vector('theta').size-1)
 			for ky_element in 0...gm.shape[0]
 				#p phi_t[ky_element].transpose[0]
 				spectrum = GSL::Vector::Complex.alloc(phi_t[ky_element]).forward.square
 				if options[:no_kpar0]
 					spectrum[0]=0.0
 				end
+        #ep spectrum.size
 				spectrum = spectrum.from_box_order
 				#ep spectrum.shape
 				spectrum = spectrum*gvky[ky_element]**2 unless options[:phi2_only]
+        #ep gm.size
+        #ep spectrum.size
 				gm.set_row(ky_element, spectrum)
 			end
 			if options[:no_zonal]

data/lib/gs2crmod/gsl_tools.rb

@@ -35,12 +35,12 @@ class GSL::Vector
 	
 	def from_box_order
 		size = self.size
-		v1, v2 = self.subvector(0, (size+1)/2), self.subvector((size+1)/2, (size-1)/2)
+		v1, v2 = self.subvector(0, (size+2)/2), self.subvector((size+2)/2, (size-1)/2)
 		return v2.connect(v1)
 	end
 	def to_box_order
 		size = self.size
-		v1, v2 = self.subvector(0, (size-1)/2), self.subvector((size-1)/2, (size+1)/2)
+		v1, v2 = self.subvector(0, (size-1)/2), self.subvector((size-1)/2, (size+2)/2)
 		return v2.connect(v1)
 	end
 

data/lib/gs2crmod/spectrogk/namelists.rb

@@ -2030,6 +2030,46 @@
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer},
+     :iky_init=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :tests=>["Tst::INT"],
+       :code_name=>:iky_init,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer},
+     :ikpar_init2=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :tests=>["Tst::INT"],
+       :code_name=>:ikpar_init2,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer},
+     :ikx_init2=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :tests=>["Tst::INT"],
+       :code_name=>:ikx_init2,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer},
+     :iky_init2=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :tests=>["Tst::INT"],
+       :code_name=>:iky_init2,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer},
      :force_single_kpar=>
       {:should_include=>"true",
        :description=>

data/test/test_gs2crmod.rb

@@ -167,6 +167,9 @@ class TestAgkAnalysis < Test::Unit::TestCase
 		#kit.gnuplot
 		assert_equal(126, kit.data[0].y.data.size)
 		assert_equal(@runner.run_list[1].netcdf_file.var('phi2').get('start' => [4], 'end' => [4]).to_a[0], kit.data[0].y.data[4])
+    assert_equal(nil,@runner.run_list[1].instance_variable_get(:@shat))
+		kit = @runner.run_list[1].graphkit('kpar_spectrum',{})
+		#kit.gnuplot
 	end
 	def test_analysis
 		assert_equal(1, @runner.run_list.size)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.9.2
+  version: 0.9.4
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-31 00:00:00.000000000 Z
+date: 2013-08-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: &10308540 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,21 +22,15 @@ dependencies:
         version: 0.12.16
   type: :runtime
   prerelease: false
-  version_requirements: *10308540
-- !ruby/object:Gem::Dependency
-  name: ruby-netcdf
-  requirement: &10307700 !ruby/object:Gem::Requirement
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.6.6.1
-  type: :runtime
-  prerelease: false
-  version_requirements: *10307700
+        version: 0.12.16
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &10306140 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +38,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *10306140
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &10247600 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +54,15 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *10247600
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &9765940 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -66,10 +70,15 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *9765940
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &9764800 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,7 +86,12 @@ dependencies:
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *9764800
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.8.4
 description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
   be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated
   running and analysis of large simulations. This module allows GS2 (and its sister
@@ -166,7 +180,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.11
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.